multiple instances of the same sequence

I've generated a database of exon2 sequences from MHC class I genes,
and am adding to it new sequences from a cloning project which picks
up sequences from more than a single locus. If I enter a new sequence
that is identical to one already in the database, what effect does
that have on the tree generated? That is, will the calculations be
biased if multiple instances of the same or nearly identical sequenes
are entered?
-John Rodgers
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